Figure 1

Chikungunya virus is found in MARCO-expressing floor lymphatic endothelial cells in the draining lymph node at 8 hpi

A. UMAP projection shows the fraction of counts aligning to the CHIKV genome for the 8 hpi timepoint.

B. CHIKV counts are shown for cell types with >50 cells for the 8 hpi CHIKV-infected sample.

C. UMAP projection shows CHIKV-high cells (>0 CHIKV counts) for the 8 hpi timepoint.

D. MARCO expression is shown for fLECs for mock-infected cells and CHIKV-infected cells classified as either CHIKV low or CHIKV high. P values were calculated using a two-sided Wilcoxon rank-sum test with Bonferroni correction. In the boxplot, the central lines, the box limits, and the whiskers represent medians, the interquartile range (IQR), and min/max values that are not outliers, respectively. Outliers are shown as points and include any values that are more than 1.5× IQR away from the box.


Figure S1

CHIKV may target MARCO-expressing LECs for infection

Version 1

A. UMAP projection shows CHIKV sgRNA ratio (sgRNA counts / 5’ counts) for the 24 hpi timepoint.

B. CHIKV sgRNA ratio is shown for cells with >0 sgRNA counts and >0 5’ counts. Cell types with at least 10 cells are shown.

C. The correlation between CHIKV sgRNA ratio and QC metrics is shown for CHIKV-high cells.

D. The expression of select marker genes is shown for the 8 hpi and 24 hpi timepoints.


Version 2

Extended version of Figure S1

A. UMAP projection shows annotated cell types for the 24 hpi timepoint.

B. UMAP projection shows CHIKV sgRNA ratio (sgRNA counts / 5’ counts) for the 24 hpi timepoint.

C. The fraction of cells identified as CHIKV-high is shown for each cell type for the 24 hpi timepoint.

D. CHIKV sgRNA ratio is shown for cells with >0 sgRNA counts and >0 5’ counts. Cell types with >10 cells are shown.

E. The correlation between CHIKV sgRNA ratio and QC metrics is shown for CHIKV-high cells.


Extended cell type annotation figure

A. The correlation between annotated LEC subsets and reference data is shown for the 8 hpi and 24 hpi timepoint.

B. The expression of select marker genes is shown for the 8 hpi and 24 hpi timepoints.


Figure 5

CHIKV infection induces distinct cell type-specific gene expression programs

A. The average fold change in expression is shown below for the top 6 CHIKV-induced gene expression programs. Fold changes were scaled and centered for each gene (row). A darker tile indicates the gene is more strongly upregulated in the cell type (e.g. the Marco LEC cluster includes genes that are generally more highly upregulated in Marco LECs)

B. The top 6 gene ontology terms are shown for the gene expression programs described in A.

C. Select genes identified in A are shown below for mock- and CHIKV-infected samples. p-values comparing mock- and CHIKV-infected samples are shown above each set of boxplots.

Brief description of approach:

  1. Upregulated genes for each cell type were identified by comparing mock- and CHIKV-infected samples. To be included, a gene must have an adjusted p-value <0.05 for all replicates and >1.25 fold increase in expression for all replicates.
  2. Hierarchical clustering was used to divide upregulated genes into 10 groups based on their average fold change in expression for each cell type.
  3. The top 7 clusters are shown below. The top 2 clusters (based on number of genes) appeared functionally similar and were merged into one cluster (interferon response).